Bst polymerase for whole genome amplification
Supplemental materials
Evaluation of whole-community genome DNA amplification methods with microarrays
Jian Wang
1, 2
, Joy D. Van Nostrand
2, 3
, Liyou Wu
2, 3
, Zhili He
2, 3
,
Guanghe Li
1
, and Jizhong Zhou
1, 2, 3, *
1 School of Environment, Tsinghua University, Beijing, China
2 Institute for Environmental Genomics, University of Oklahoma, Norman,
OK
3 Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley,
CA 94720
*Corresponding author: Dr. Jizhong Zhou
Institute for Environmental Genomics (IEG)
Department of Botany and Microbiology
University of Oklahoma
Norman, OK 73019
Phone: 405-325-6073
Fax: 405-325-7552
E-mail: jzhou@ou.edu
S1
Unamplified
A Desulfovibrio vulgaris Hildenborough
Bst REPLI-g Templiphi
Genes
Unamplified
B
Genes Genes
Rhodopseudomonas palustris CGA009
Bst REPLI-g
Genes
Templiphi
Genes Genes Genes Genes
S2
Unamplified
C Shenwanella oneidensis MR-1
Bst REPLI-g Templiphi
Genes
Unamplified
Genes Genes
D Thermoanaerobacter ethanolicus X514
Bst REPLI-g
Genes
Templiphi
Genes Genes Genes Genes
FIG. S1. Ratio of signal intensity of Cy5 to Cy3 (unamplfied DNA, DNA amplified by Bst, REPLI-g and Templiphi to unamplified DNA) of individual gene for pure culture genome. (A) Desulfovibrio vulgaris
Hildenborough, (B) Rhodopseudomonas palustris CGA009, (C) Shenwanella
oneidensis MR-1 and (D) Thermoanaerobacter ethanolicus X514.
S3
10
1
0.1
Bst
Bst _S
REPLI-g Templiphi
Templiphi_S
REPLI-g_S
Genes Genes Genes
FIG. S2. Ratio of signal intensity of amplified to unamplified DNA (DNA amplified by Bst, REPLI-g and Templiphi to unamplified DNA) of individual gene detected by GeoChip for the community sample. Bst: amplified with Bst, Bst_S: amplified with Bst and sonicated before labeling,
REPLI-g: amplified with REPLI-g, REPLI-g_S: amplified with REPLI-g and sonicated before labeling, Templiphi: amplified with Templiphi,
Templiphi_S.
S4
Bst vs REPLI-g
4
Bst vs Templiphi
4 4
REPLI-g vs Templiphi
0.125
1
1 8
0.125
1
1 8 0.125
1
1
R² = 0.1376
0.25
0.25
R² = 0.1742
0.25
R² = 0.1393
FIG. S3. Scatter plot of Cy5/Cy3 ratios of biased genes in aDNA amplified by the three MDA methods. DNA of Shenwanella oneidensis MR-1 was used as the template.
The genes whose Cy5/Cy3 ratios in any aDNA showed >1 fold are defined as biased genes. The results suggested that the different MDA methods would produce different biased genes.
8
S5
Rep1 vsRep2
4
Rep2 vsRep3
4
0.25
1
1 4 0.25
1
1
R² = 0.965
R² = 0.9679
0.25
0.25
FIG. S4. Scatter plot of Cy5/Cy3 ratio of biased genes in aDNA amplified by
Bst in different technical replicates. DNA of Shenwanella oneidensis MR-1 was used as the template. The genes whose Cy5/Cy3 ratios in any replicates showed >1 fold are defined as biased genes. The results suggested that the bias produced by one MDA method would be reproducible.
S6
4
